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Developmental variation of the SUUR protein binding correlates with gene regulation and specific chromatin types in D. melanogaster

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Abstract

Eukaryotic genomes are organized in large chromatin domains that maintain proper gene activity in the cell. These domains may be permissive or repressive to the transcription of underlying genes. Based on its protein makeup, chromatin in Drosophila cell culture has been recently categorized into five color-coded states. Suppressor of Under-Replication (SUUR) protein was found to be the major component present in all three repressive chromatin states named BLACK, BLUE, and GREEN and to be depleted from the active YELLOW and RED chromatin types. Here, we addressed the question of developmental dynamics of SUUR binding as a marker of repressed chromatin types. We established genomewide SUUR binding profiles in larval salivary gland, brain, and embryos using DNA adenine methyltransferase identification (DamID) technique, performed their pairwise comparisons and comparisons with the published data from Drosophila Kc cells. SUUR binding pattern was found to vary between the samples. Increase in SUUR binding predominantly correlated with local gene repression suggesting heterochromatin formation. Reduction in SUUR binding often coincided with activation of tissue-specific genes probably reflecting the transition to permissive chromatin state and increase in accessibility to specific transcription factors. SUUR binding plasticity accompanied by the regulation of the underlying genes was mainly observed in BLACK, BLUE, and RED chromatin types. Our results provide novel insight into the developmental dynamics of repressive chromatin and reveal a link to the chromatin-guided regulation of gene expression.

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Acknowledgments

We thank Dr. Tim Westwood and Canadian Drosophila Microarray Center who performed microarray hybridizations and Dr. Bas van Steensel for Dam-containing vectors. The datasets for this paper have been deposited at NCBI under the reference series GSE33873. The work was supported by the Russian Foundation for Basic Research grants 12-04-00160, 12-04-33080, and 12-01-31128 and by the Program of Presidium of the Russian Academy of Sciences “Molecular and Cellular Biology” (grant no. 6.3).

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  1. Institute of Molecular and Cellular Biology SB RAS, Lavrentyev Ave., 8/2, Novosibirsk, 630090, Russia

    Daniil A. Maksimov, Dmitry E. Koryakov & Stepan N. Belyakin

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  1. Daniil A. Maksimov
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  2. Dmitry E. Koryakov
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  3. Stepan N. Belyakin
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Correspondence to Stepan N. Belyakin.

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Supplementary Figure 1

hsp70 promoter from pUAST vector ensures a very low level of Dam-Myc expression. Western blot detection of Dam-Myc protein with the anti-Myc-tag antibodies in salivary glands of y,w strain (negative control, first lane), hsp70 > Dam-Myc strain (second lane) and in hsp70 > Dam-Myc strain induced with salivary gland-specific AB1 Gal4 driver (positive control, third lane). anti-Tubuline antibodies were used as a load control. Asterisk shows a non-specific band appearing due to over-exposure of the membrane. (JPEG 69 kb)

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Supplementary Figure 2

Effect of data normalization. A – distribution of the raw DamID data in the four samples. B – the same after the normalization step. Scale – Log2(Dam-Myc-SUUR/Dam-Myc). C – K-means clustering of the normalized data in the four samples reveals a substantial variation of SUUR binding in different cell types. (JPEG 750 kb)

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Supplementary Figure 3

Examples of SUUR profile variability in different biological samples. The colors and legends are the same as on the Fig. 1. (JPEG 496 kb)

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Supplementary Figure 4

Correlation of SUUR binding dynamics and gene activity in six pairs of samples. The legend is the same as in Fig. 3c. (JPEG 581 kb)

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Supplementary Figure 5

Variability of SUUR binding near the borders and towards the centers of domains in different chromatin types. Portions of differentially bound genes in 1 kb bins starting from the borders of the domains of different types are presented. No differences from the distributions presented in the Fig.  5a were found indicating that observed variation of SUUR binding is not a bias stemming from the domain borders. (JPEG 457 kb)

High Resolution Image (EPS 936 kb)

Supplementary Figure 6

A test study of H3K36me3 variability between Kc cells and 0-12h embryos. A – distribution of H3K36me3 histone mark across five chromatin types. B – variability of H3K36me3 levels in five chromatin types assessed with the same analytic tools as for SUUR. GREEN chromatin tends to loose H3K36me3 in embryos while BLUE chromatin accumulates H3K36me3. Other chromatin types do not follow this pattern. This picture is strikingly different from the observed variability of SUUR (Fig.  5a). (JPEG 227 kb)

High Resolution Image (EPS 585 kb)

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Supplementary Table 3

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Supplementary Table 5

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Maksimov, D.A., Koryakov, D.E. & Belyakin, S.N. Developmental variation of the SUUR protein binding correlates with gene regulation and specific chromatin types in D. melanogaster . Chromosoma 123, 253–264 (2014). https://doi.org/10.1007/s00412-013-0445-6

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